Parameterization results




Atoms

RMSD Maximum deviation Average deviation Pearson2 Number of atoms
Parameterization0.0791 0.9498 0.0534 0.9592 122751
Validation0.0854 1.1354 0.0565 0.9536 13639

Molecules

RMSD Maximum deviation Average deviation Pearson2 Number of molecules Smallest molecule atoms Largest molecule atoms Average number of atoms
Parameterization0.0741 0.2094 0.0546 0.9568 4027 5 124 30.482
Validation0.0768 0.2173 0.057 0.9543 448 9 100 30.4442

Atomic types - Parameterization

Atomic type RMSD Maximum deviation Average deviation Pearson2 Number of atoms %
Br0.04970.13840.03620.39172730.22
C0.08820.67380.06570.9144831139.36
Cl0.06020.31940.04740.67449840.8
F0.06540.30820.03870.43718180.67
H0.04360.2110.03050.66325141141.88
I0.04420.17010.03280.27415551.27
N0.11810.49460.09420.874770865.77
O0.08870.47180.06280.816797847.97
P0.35240.94980.26460.77983490.28
S0.17080.60450.1370.971621801.78

Atomic types - Validation

Atomic type RMSD Maximum deviation Average deviation Pearson2 Number of atoms %
Br0.04450.15720.02910.4934630.46
C0.0940.59640.06830.8946535139.23
Cl0.05980.26860.04650.68461000.73
F0.07740.22010.05030.4661200.88
H0.04890.20930.03380.6154570841.85
I0.04840.13160.03560.17981791.31
N0.12790.44320.09930.87467935.81
O0.09320.4030.06430.794810257.52
P0.36391.13540.2680.7722550.4
S0.17910.57240.14060.96832451.8

Legend: RMSD < 0.05 < 0.1 < 0.15 < 0.2 < 0.3 < 0.4 >= 0.4


Type Count %
C-H4645136.81
C-C4315234.2
C-N111708.85
C-O82086.5
H-N33012.62
C-S25432.02
O-S20191.6
C-I15511.23
H-O14381.14
N-O12480.99
N-N8740.69
C-Cl7860.62
C-F7050.56
O-P6660.53
C-P3760.3
N-S3720.29
Br-C2450.19
S-S2260.18
H-S2060.16
N-P1990.16
Cl-S1210.1
F-S1090.09
O-O910.07
Cl-N770.06
Br-N280.02
H-P150.01
F-P40.0
I-O30.0
P-P20.0
I-N10.0

Set of molecules: DTP_large.sdf
Method: EEM
Optimization method: guided_minimization
Subset heuristic: 5
Samples: 500000
Minimization method: SLSQP
Date of parameterization: 2019-04-04 10:58
Time: 0:23:21
Number of cpu: 4
Command: ./mach.py --mode parameterization --method EEM --optimization_method guided_minimization --minimization_method SLSQP --parameters EEM.json --sdf DTP_large.sdf --ref_charges DTP_large.chg --data_dir results_data --cpu 4 --git_hash 2dc647db55f085e398df3be292a61ce3f46d7847 --atomic_types_pattern plain --subset_heuristic 5 --num_of_samples 500000 --validation 10
Github commit hash: 2dc647db55f085e398df3be292a61ce3f46d7847

parameters.json


Original parameters file

original_parameters.json

SDF file

DTP_large.sdf

Empirical charges file

DTP_large_EEM.chg

Reference charges file

DTP_large.chg

Molecules logs

molecules.log
Author: Ondrej Schindler
Email: dargen3@centrum.cz
Source code: https://github.com/dargen3/MACH
Licence: None